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synced 2025-10-20 13:43:47 +08:00
Include EMBL example with max length line wrapping, and fix previous commit
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peterjc
@ -303,22 +303,22 @@ class _InsdcWriter(SequentialSequenceWriter):
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"Returns a list of strings."""
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#TODO - Do the line spliting while preserving white space?
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text = text.strip()
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if len(text) < max_len:
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if len(text) <= max_len:
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return [text]
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words = text.split()
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assert max([len(w) for w in words]) <= max_len, \
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"Your description cannot be broken into nice lines!:\n%s" \
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% repr(text)
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if max([len(w) for w in words]) > max_len:
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raise ValueError("Text cannot be broken into len %i lines!:\n%s"
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% (max_len, repr(text)))
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text = ""
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while words and len(text) + 1 + len(words[0]) < max_len:
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while words and len(text) + 1 + len(words[0]) <= max_len:
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text += " " + words.pop(0)
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text = text.strip()
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assert len(text) <= max_len
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answer = [text]
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while words:
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text = ""
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while words and len(text) + 1 + len(words[0]) < max_len:
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text = words.pop(0)
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while words and len(text) + 1 + len(words[0]) <= max_len:
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text += " " + words.pop(0)
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text = text.strip()
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assert len(text) <= max_len
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@ -356,7 +356,7 @@ class GenBankWriter(_InsdcWriter):
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def _write_single_line(self, tag, text):
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"Used in the the 'header' of each GenBank record."""
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assert len(tag) < self.HEADER_WIDTH
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assert len(text) < self.MAX_WIDTH - self.HEADER_WIDTH, \
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assert len(text) <= self.MAX_WIDTH - self.HEADER_WIDTH, \
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"Annotation %s too long for %s line" % (repr(text), tag)
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self.handle.write("%s%s\n" % (tag.ljust(self.HEADER_WIDTH),
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text.replace("\n", " ")))
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@ -366,9 +366,8 @@ class GenBankWriter(_InsdcWriter):
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#TODO - Do the line spliting while preserving white space?
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max_len = self.MAX_WIDTH - self.HEADER_WIDTH
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lines = self._split_multi_line(text, max_len)
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assert len(tag) < self.HEADER_WIDTH
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self._write_single_line(tag, lines[0])
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for line in lines[1:] :
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for line in lines[1:]:
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self._write_single_line("", line)
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def _write_multi_entries(self, tag, text_list):
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@ -259,3 +259,45 @@ SQ Sequence 153 AA; 17492 MW; 2159E552 CRC32;
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KNTTEKETFC RAATVLRQFY SHHEKDTRCL GATAQQFHRH KQLIRFLKRL DRNLWGLAGL 120
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NSCPVKEANQ STLENFLERL KTIMREKYSK CSS 153
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//
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ID CQ797900; SV 1; linear; protein; PRT; PRO; 496 AA.
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XX
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AC CQ797900;
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XX
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DT 20-APR-2004 (Rel. 79, Created)
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DT 31-MAY-2006 (Rel. 88, Last updated, Version 3)
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XX
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DE Sequence 2 from Patent WO2004029250.
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XX
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KW .
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XX
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OS Sinorhizobium meliloti
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OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Rhizobiaceae;
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OC Sinorhizobium/Ensifer group; Sinorhizobium.
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XX
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RN [1]
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RA Hoshino T., Ichikawa K., Tazoe M.;
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RT "Dna encoding
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RT flavin-adenine-dinucleotide-dependent-d-erythronate-4-phosphate-dehydrogena
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RT se , pdxr , and microbial production of vitamin b6";
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RL Patent number WO2004029250-A1/2, 08-APR-2004.
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RL DSM IP Assets B.V. (NL).
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XX
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FH Key Location/Qualifiers
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FH
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FT source 1..496
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FT /organism="Sinorhizobium meliloti"
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FT /mol_type="protein"
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FT /db_xref="taxon:382"
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XX
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SQ Sequence 496 AA; 53189 MW; 54C0D9AD CRC32;
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MAIGTLEATT LIRGRAMTTV LPSPELIASF VDIVGPGNAL TAPADTAPYL VESRGLYRGT 60
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TPLVLRPGSV EEVSLVMRLA SQTRTAVVPQ GGNTGHVAGQ IPREGKADVV LSLERLNRIR 120
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DIDPVGNVIV ADAGCILADI QKAADDVDRL FPLSLGSEGS ARIGGNLSTN AGGTAVLAYG 180
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NMRQLCLGLE VVLPTGEIWD GLRRLRKDNT GYDLRDLFIG AEGTLGVITG AVLKLFPKPR 240
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GHQVAFAGLR SVEDALTLFD RATSVCGPAL TGFELMPRLG IEFTTRHIAG VRDPMETTHP 300
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WYALIDISTS DTAESAERMV QDLLEAVIAD GLVENAVIAQ NEAQRRALWH MRESMSPAQK 360
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PEGGSIKHDV SVPVSSIPAF MTEADALVSK AIPGARICAF GHMGDGNIHY NISQPVGADK 420
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QSFLDRWREI NAIVHAVVLK HDGSISAEHG IGQLKRDELA AIRSPIEIEL MRRIKHAFDP 480
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AGIMNPDKVL REDRGE 496
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//
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@ -1789,7 +1789,7 @@ Testing reading genbank format file GFF/NC_001422.gbk
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Failed: Missing SFF flow information
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Checking can write/read as 'tab' format
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Checking can write/read as 'nexus' format
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Testing reading embl format file EMBL/epo_prt_start.embl
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Testing reading embl format file EMBL/epo_prt_selection.embl
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ID = 'A00022.1', Name='A00022',
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Seq='CLARIIRYFYNAKA', length=14
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ID = 'A00028.1', Name='A00028',
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@ -1797,8 +1797,8 @@ Testing reading embl format file EMBL/epo_prt_start.embl
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ID = 'A00031.1', Name='A00031',
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Seq='RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRA...ERTCGGA', length=58
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...
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ID = 'A00078.1', Name='A00078',
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Seq='MGLTSQLLPPLFFLLACAGNFVHGHKCDITLQEIIKTLNS...KYSKCSS', length=153
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ID = 'CQ797900.1', Name='CQ797900',
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Seq='MAIGTLEATTLIRGRAMTTVLPSPELIASFVDIVGPGNAL...LREDRGE', length=496
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Checking can write/read as 'fasta' format
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Checking can write/read as 'clustal' format
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Failed: Sequences must all be the same length
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@ -1808,17 +1808,19 @@ Testing reading embl format file EMBL/epo_prt_start.embl
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Failed: Sequences must all be the same length
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Checking can write/read as 'embl' format
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Checking can write/read as 'fastq' format
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A00078.1).
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
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Checking can write/read as 'fastq-illumina' format
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A00078.1).
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
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Checking can write/read as 'fastq-solexa' format
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A00078.1).
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
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Checking can write/read as 'genbank' format
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Failed: Text cannot be broken into len 68 lines!:
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'Dna encoding flavin-adenine-dinucleotide-dependent-d-erythronate-4-phosphate-dehydrogena se , pdxr , and microbial production of vitamin b6'
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Checking can write/read as 'imgt' format
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Checking can write/read as 'phd' format
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A00078.1).
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
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Checking can write/read as 'qual' format
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=A00078.1).
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Failed: No suitable quality scores found in letter_annotations of SeqRecord (id=CQ797900.1).
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Checking can write/read as 'sff' format
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Failed: Missing SFF flow information
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Checking can write/read as 'tab' format
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@ -139,7 +139,7 @@ test_files = [ \
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#Following files are also used in test_GFF.py
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("genbank",False, 'GFF/NC_001422.gbk', 1),
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#Following files are currently only used here or in test_SeqIO_index.py:
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("embl", False, 'EMBL/epo_prt_start.embl', 8), #proteins
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("embl", False, 'EMBL/epo_prt_selection.embl', 9), #proteins
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("embl", False, 'EMBL/TRBG361.embl', 1),
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("embl", False, 'EMBL/DD231055_edited.embl', 1),
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("embl", False, 'EMBL/SC10H5.embl', 1), # Pre 2006 style ID line
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@ -128,7 +128,7 @@ tests = [
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("Quality/sanger_faked.fastq", "fastq-sanger", generic_dna),
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("Quality/solexa_faked.fastq", "fastq-solexa", generic_dna),
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("Quality/illumina_faked.fastq", "fastq-illumina", generic_dna),
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("EMBL/epo_prt_start.embl", "embl", None),
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("EMBL/epo_prt_selection.embl", "embl", None),
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("EMBL/U87107.embl", "embl", None),
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("EMBL/TRBG361.embl", "embl", None),
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("EMBL/A04195.imgt", "embl", None), #Not a proper EMBL file, an IMGT file
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